Buggy code:
public int getGenomeGuidedMinCoverage ( ) { } public void setGenomeGuidedMinCoverage ( int genomeGuidedMinCoverage ) { } public int getCmdsPerNode ( ) { } public void setCmdsPerNode ( int cmdsPerNode ) { } public int getMaxGridNodes ( ) { } public void setMaxGridNodes ( int maxGridNodes ) { } public File getGridConfFile ( ) { } public void setGridConfFile ( File gridConfFile ) { } public int getGridNodeCpu ( ) { } public void setGridNodeCpu ( int gridNodeCpu ) { } public String getGridNodeMaxMemory ( ) { } public void setGridNodeMaxMemory ( String gridNodeMaxMemory ) { } @ Override protected void setOptionFromMapEntry ( ConanParameter param , String value ) { } @ Override protected void setArgFromMapEntry ( ConanParameter param , String value ) { } @ Override public void parseCommandLine ( CommandLine cmdLine ) { } @ Override public ParamMap getArgMap ( ) { ParamMap pvp = new DefaultParamMap ( ) ; if ( ( this . seqType ) != null ) { pvp . put ( params . getSeqType ( ) , this . seqType . toArgString ( ) ) ; } pvp . put ( params . getMaxMemory ( ) , ( ( Integer . toString ( this . maxMemory ) ) + "G" ) ) ; if ( ( this . leftInput ) != null ) { pvp . put ( params . getLeftInput ( ) , this . leftInput . getAbsolutePath ( ) ) ; } if ( ( this . rightInput ) != null ) { pvp . put ( params . getRightInput ( ) , this . rightInput . getAbsolutePath ( ) ) ; } if ( ( this . singleInput ) != null ) { pvp . put ( params . getSingleInput ( ) , this . singleInput . getAbsolutePath ( ) ) ; } if ( ( this . ssLibType ) != null ) { pvp . put ( params . getSsLibType ( ) , this . ssLibType . toString ( ) ) ; } if ( ( this . output ) != null ) { pvp . put ( params . getOutput ( ) , this . output . getAbsolutePath ( ) ) ; } if ( ( this . cpu ) > ( TrinityV2 . Args . DEFAULT_CPUS ) ) { pvp . put ( params . getCpu ( ) , Integer . toString ( this . cpu ) ) ; } if ( ( ( this . minContigLength ) != ( TrinityV2 . Args . DEFAULT_MIN_CONTIG_LENGTH ) ) && ( ( this . minContigLength ) > 0 ) ) { pvp . put ( params . getMinContigLength ( ) , Integer . toString ( this . minContigLength ) ) ; } if ( ( this . kmerSize ) != ( TrinityV2 . Args . DEFAULT_KMER_SIZE ) ) { pvp . put ( params . getKmerSize ( ) , Integer . toString ( this . kmerSize ) ) ; } if ( ( this . genomeGuidedBam ) != null ) { pvp . put ( params . getGenomeGuidedBam ( ) , this . genomeGuidedBam . getAbsolutePath ( ) ) ; } if ( this . normaliseReads ) { pvp . put ( params . getNormaliseReads ( ) , Boolean . toString ( this . normaliseReads ) ) ; } if ( this . trimmomatic ) { pvp . put ( params . getTrimmomatic ( ) , Boolean . toString ( this . trimmomatic ) ) ; } if ( this . jaccardClip ) { pvp . put ( params . getJaccardClip ( ) , Boolean . toString ( this . jaccardClip ) ) ; } if ( this . fullCleanUp ) { pvp . put ( params . getFullCleanUp ( ) , Boolean . toString ( this . fullCleanUp ) ) ; } <START_BUG> if ( ( this . genomeGuidedMaxIntron ) != ( TrinityV2 . Args . DEFAULT_MAX_INTRON_SIZE ) ) { <END_BUG> pvp . put ( params . getGenomeGuidedMaxIntron ( ) , Integer . toString ( this . genomeGuidedMaxIntron ) ) ; } if ( ( this . genomeGuidedMinCoverage ) != ( TrinityV2 . Args . DEFAULT_GENOME_GUIDED_MIN_COVERAGE ) ) { pvp . put ( params . getGenomeGuidedMinCoverage ( ) , Integer . toString ( this . genomeGuidedMinCoverage ) ) ; } if ( ( ( this . inchwormMinKmerCoverage ) != ( TrinityV2 . Args . DEFAULT_INCHWORM_MIN_KMER_CVG ) ) && ( ( this . inchwormMinKmerCoverage ) > 0 ) ) { pvp . put ( params . getInchwormMinKmerCoverage ( ) , Integer . toString ( this . inchwormMinKmerCoverage ) ) ; } if ( ( ( this . butterflyGroupPairsDistance ) != ( TrinityV2 . Args . DEFAULT_BUTTERFLY_GROUP_PAIRS_DISTANCE ) ) && ( ( this . butterflyGroupPairsDistance ) > 0 ) ) { pvp . put ( params . getButterflyGroupPairsDistance ( ) , Integer . toString ( this . butterflyGroupPairsDistance ) ) ; } if ( ( ( this . butterflyPathReinforcementDistance ) != ( TrinityV2 . Args . DEFAULT_BUTTERFLY_PATH_REINF_DISTANCE ) ) && ( ( this . butterflyPathReinforcementDistance ) > 0 ) ) { pvp . put ( params . getButterflyPathReinforcementDistance ( ) , Integer . toString ( this . butterflyPathReinforcementDistance ) ) ; } if ( ( this . gridConfFile ) != null ) { pvp . put ( params . getGridConfFile ( ) , this . gridConfFile . getAbsolutePath ( ) ) ; } if ( ( this . gridNodeCpu ) != ( TrinityV2 . Args . DEFAULT_GRID_NODE_CPU ) ) { pvp . put ( params . getGridNodeCpu ( ) , Integer . toString ( this . gridNodeCpu ) ) ; } if ( ! ( this . gridNodeMaxMemory . equalsIgnoreCase ( TrinityV2 . Args . DEFAULT_GRID_NODE_MAX_MEMORY ) ) ) { pvp . put ( params . getGridNodeMaxMemory ( ) , this . gridNodeMaxMemory . toUpperCase ( ) ) ; } return pvp ; } } public static class Params extends AbstractProcessParams { private ConanParameter seqType ; private ConanParameter maxMemory ; private ConanParameter leftInput ; private ConanParameter rightInput ;

Fix:
if ( ( this . genomeGuidedBam ) != null ) {